Agriculture: Floriculture and Ornamental Nurseries Pest Management Guidelines

Management of Soilborne Pathogens

Soil is a reservoir for many plant pathogens and plants are under regular attack by these soilborne organisms. If inoculum levels are high enough and environmental conditions become favorable for infection, susceptible plants will develop disease. Soilborne pathogens are readily spread if infested soil or contaminated water moves into other fields or planting areas. Levels of soilborne pathogens, including bacteria, fungi, nematodes, and some viruses can be reduced in the soil by appropriate treatments.

Learn which pathogens attack the crop to be grown. Examine the crop regularly, at least weekly, for symptoms of disease or signs of pathogens.

To monitor for root diseases in floriculture and ornamental nurseries

  • Select a few plants from different locations, remove plants from their containers, and gently scrape or wash away soil.
  • Examine roots and crowns for discoloration, softness, shriveling, or other early indications of disease.
  • Know what healthy roots look like so diseased roots can be detected early. Healthy root characteristics may change or be different depending on species, root age, or growing conditions.
  • Look for discolored or wilted plants and fungal growths aboveground, which may indicate more advanced stages of disease.
  • Use test kits in combination with other information to make good pest management decisions. Test kits are readily available for detecting Phytophthora pathogens infecting greenhouse and container-grown nursery plants. Agdia (Elkhart, IN) supplies simple immunological test kits that detect Phytophthora species in minutes. A positive detection can usually help with the diagnostic process and get you quickly on the path to managing the problem. Sometimes, however, a positive result might be deceiving because these tests are not entirely accurate and can occasionally react to certain Pythium or Phytopythium species. These latter two groups of species may or may not be the primary cause of root disease or even a problem at all. Some of these are soil microbes that only break down already dead material, and many we do not fully understand yet. A non-positive reaction of the immunological test might be deceiving also. Sometimes the tested root tissue may not have been sampled from infected root pieces, and certain Phytophthora species do not react with the tests.
  • Send a sample of diseased plants and their roots to an appropriate laboratory to test for the presence and identification of pathogens. Proper diagnosis is vital to making the correct management decisions.

Understand the conditions and practices that promote disease and regularly examine for and remedy disease-promoting conditions and practices. Poor sanitation, inadequate drainage, and improper irrigation are the primary conditions that promote diseases of roots. Remove crop residue and old or low-quality plants that will not be marketed.

Soil Solarization

In warmer climatic areas, solarization has been effective for disinfesting containerized soil or growing medium, soil in cold frames, and soil in open fields.

For soil in containers

  • Use either in bags or flats covered with transparent plastic or in layers 3- to 9-inches wide sandwiched between two sheets of plastic to solarize planting media. A double layer of plastic can increase soil temperature by up to 50°F.
  • Monitor the temperature of the growing medium closely by placing a temperature-measuring probe into the center of the mass of the soil mix to ensure the temperature is high enough to control pests.
  • In warmer areas of California, soil inside black plastic sleeves can reach 158°F (70°C) during solarization, equivalent to target temperatures for soil disinfestation by aerated steam. At this temperature, soil is effectively solarized within 30 minutes. At 140°F (60°C), soil is solarized in 1 hour.

In open fields, soil is more easily covered with a single layer of transparent plastic. Soil temperatures will be highest at the soil surface (first 12 inches). The plastic needs to be left in place for 4 to 6 weeks. For maximum effectiveness and treatment predictability, solarize open fields only in warmer climatic areas, unless previous testing has given consistently desirable results. The effectiveness of solarization, especially in cooler climatic areas, can be improved by adding various botanical products containing glucosinolates, such as mustard seed meal, broccoli, and cabbage. Solarization is acceptable where a non-chemical approach is desired.


Heating the soil is very effective and the soil can be used immediately after cooling, unlike chemically treated soil. Many plant pathogens are killed by short exposures to high temperatures. Most plant pathogens can be killed by temperatures of 140°F (60°C) for 30 minutes. However, some viruses such as Tobacco mosaic virus (TMV) may survive this treatment. Where weed seeds are a problem, a higher treatment temperature is required, and even then, some weed seeds may still survive.

Although pure steam at sea level is at 212°F (100°C), the temperature of the steam used to treat soil is usually about 180°F because of air that is present in the steam or soil being treated. If air is mixed with steam, the temperature of the steam-air mixture can be closely controlled, depending on the ratio of air to steam. It has been demonstrated that some diseases, such as Rhizoctonia damping-off, are much less severe in soil that has been treated at 140°F rather than at 180°F. Experience will tell the grower which temperature will best treat the soil, but as a starting point try 140°F (60°C) for 30 minutes.

If a cement mixer is used to heat a bulk quantity of soil, generally it is not necessary to introduce air into the steam because a large amount of air is present in the mixer and the temperature can be controlled by simply regulating the flow of steam. Expensive air blowers are not required for this method.

Steam heating of containers filled with soil in vaults likewise may not require the introduction of air into the steam to control the temperature. However, circulation within the vault is important to ensure even distribution of heat. Circulating fans can be located within, or external to, the vault and the steam can be introduced into the recirculating air. Leave space between the vaults and check temperatures throughout the vault to ensure that there is good circulation of steam air.

Soil Fumigants

Only three fumigants with very limited suitability for soil fumigation remain allowed in California. Registered fumigants are chloropicrin, 1,3-dichloropropene (1,3-D), and methyl isothiocyanate (MITC) generators such as metam sodium, metam potassium, and Basamid. However, these products have many statewide regulatory restrictions and are also subject to local regulations. In the absence of methyl bromide, the most promising registered fumigants are chloropicrin alone or chloropicrin mixed with 1,3-dichloropropene applied sequentially in combination with metam sodium or metam potassium. These fumigants can be applied to the raised beds through drip irrigation systems. In drip fumigation, it is critical to distribute the water evenly throughout the field and throughout the target soil treatment zone. Chloropicrin and 1,3-dichloropropene should not be applied simultaneously with metam sodium to avoid their rapid degradation in the irrigation water. Only certified applicators can apply fumigants.

Metam-sodium (Vapam), and dazomet (Basamid) alone are not very effective for controlling many soilborne pathogens, including Verticillium and Fusarium oxysporum. See the Activity of Soil Fumigants table for how effective each fumigant is against various types of pests.

Chloropicrin (trichloronitromethane) is the best fumigant for controlling Verticillium dahliae. In the past it was combined with methyl bromide in various mixtures depending upon the organisms in the soil. If used alone, a water seal may be used to confine the gas; however, the gas is very objectionable and irritating (it is commonly known as tear gas) and, if not effectively confined, it may drift to inhabited areas. This is a restricted use material and requires a permit from the county Agricultural Commissioner to be purchased or applied.

Activity of soil fumigants.
Activity against
Common name Trade name Nematodes Fungi Weeds
chloropicrin TriClor fair excellent poor
  TriClor EC fair excellent fair*
1,3-dichloropropene Telone II fair excellent fair
1,3 dichloropropene plus chloropicrin Telone C35 excellent very good fair
  InLine excellent excellent good*
chloropicrin plus 1,3 dichloropropene Pic-Clor60 excellent excellent good*
  Pic-Clor60EC excellent excellent good*
metam sodium Vapam HL good good good
  Sectagon 42 good good good
metam potassium K-Pam HL good good good
  Sectagon-K54 good good good
dazomet Basamid good good good

* Using high rates or retentive plastic mulch (especially totally impermeable film) improves weed control.

Soil Fungicides

Some fungicides work best if incorporated before planting. Others may be incorporated or applied after sowing or planting. Some soil fungicides control a narrow range of organisms while others control a wide range of organisms. Some of the narrow range chemicals are the most effective in controlling a specific organism. Combinations are used to increase the number of organisms controlled.

The Examples of Conventional and Biological Fungicides table is not a complete list of available and active fungicides against soilborne pathogens. It provides examples of conventional and biological fungicides.

Examples of conventional and biological fungicides.
Common name
(Example trade name)
Alternaria and Phomopsis wilt Black root rot Cottony rot Cylindrocladium spp. Damping-off Foliar downy mildew Fusarium sp. Penicillium blue mold Phytophthora Pythium Rhizoctonia Root & stem rot Sclerotinia Sclerotium rolfsii Seed rot
Salts or esters of phosphorous acid (Aliette) C P
Gliocladium virens
(Chipco 26019)
(Subdue Maxx)
PCNB – pentachloronitrobenzene or quintozene (Terraclor) N N C C C
Streptomyces griseoviridis (Mycostop) C C P1 P1 P1 C C
C2 C2
Trichoderma spp.
C = control; P = partial control/suppression; N = no control
1 In the greenhouse it may suppress root rots of Pythium, Phytophthora, and Rhizoctonia.
2 Used for bulb or corm dips to control Fusarium basal rot and Penicillium blue mold

Seed Treatments

Streptomyces griseoviridis (Mycostop) is used as a seed treatment for damping-off and early root rots for ornamentals planted in fields or greenhouse. Captan is also a seed treatment, but offers only a limited protection.

Treatment of Containers and Equipment

Debris, soil, and plant material cling to containers and equipment; thoroughly wash equipment to remove all soil or planting mix particles. Heat treatment is effective in killing the plant pathogens that adhere to containers or that are in the debris. Where steam is not available, hot water or solarization can be very effective. Most plastic can be treated with hot water at temperatures that cause minimal softening. The minimum water temperature should be 140°F (60°C) whenever possible. Treatment time can be as short as 1 minute. Longer treatment times are more reliable, and the container or equipment must reach at least 140°F (60°C). For solarization, containers should be moistened, stacked, and placed beneath a double-layer tent. Incubate for 30 minutes at or above 158°F (70°C), or 1 hour at or above 140°F (60°C).

Sodium hypochlorite (the active ingredient in bleach) is effective in killing most types of fungal spores and bacteria. However, it penetrates clinging soil and plant material very poorly. It is effective only as a surface disinfectant, so containers, tools, etc. must be free of soil and plant material and clean before treatment. Sodium hypochlorite is generally used as a surface disinfectant at 0.5%. To achieve this concentration of sodium hypochlorite, household bleach can be diluted 1 part bleach to 9 parts water. For known contaminated materials, a stronger solution diluted 1 part bleach to 4 parts water (1% sodium hypochlorite), may be more effective in killing pathogens. Allow the solution to be in contact with nonporous materials for a minimum of 5 to 10 minutes, then rinse well with clean water to remove bleach and avoid phytotoxicity. Bleach dilutions must be made fresh each day because once diluted, the effectiveness of the solution diminishes over time (50% loss occurs every 2 hours). Debris, potting mix, and other residues left over in bleach washes will also greatly reduce bleach concentration and effectiveness.

Quaternary ammonia compounds are excellent bactericides and viricides and are effective in killing some kinds of fungal spores. They penetrate plant material and soil poorly, so containers, tools, etc. must be clean before treatment.

Text Updated: 11/20